Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation–Condensation to Framework Mechanism

Kmiecik, Sebastian; Koliński, Andrzej

doi:10.1021/ja203275f

Cited by 39 publications

(64 citation statements)

References 39 publications

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“…(C) The ability of DnaK to disrupt long-range contacts in the client substrate is of potential importance in the role that it plays in refolding, by converting misfolded substrates into a folding-competent conformation, and in disaggregation where DnaK unfolds the substrates and presents them to Hsp104/ClpB. study in which the effect of the chaperonin GroEL/ES on protein folding was studied (54).…”

Section: Discussionmentioning

confidence: 99%

Hsp70 biases the folding pathways of client proteins

Sekhar

Rosenzweig

Bouvignies

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The 70-kDa heat shock protein (Hsp70) family of chaperones bind cognate substrates to perform a variety of different processes that are integral to cellular homeostasis. Although detailed structural information is available on the chaperone, the structural features of folding competent substrates in the bound form have not been well characterized. Here we use paramagnetic relaxation enhancement (PRE) NMR spectroscopy to probe the existence of long-range interactions in one such folding competent substrate, human telomere repeat binding factor (hTRF1), which is bound to DnaK in a globally unfolded conformation. We show that DnaK binding modifies the energy landscape of the substrate by removing long-range interactions that are otherwise present in the unbound, unfolded conformation of hTRF1. Because the unfolded state of hTRF1 is only marginally populated and transiently formed, it is inaccessible to standard NMR approaches. We therefore developed a 1 H-based CEST experiment that allows measurement of PREs in sparse states, reporting on transiently sampled conformations. Our results suggest that DnaK binding can significantly bias the folding pathway of client substrates such that secondary structure forms first, followed by the development of longer-range contacts between more distal parts of the protein.Hsp70 | protein folding | excited states | molecular chaperones | PRE T he 70-kDa heat shock protein (Hsp70) chaperone system is an important component of the cellular proteostasis machinery, serving as a central hub to channel client proteins along folding, refolding, maturation, disaggregation, and proteolytic pathways in cooperation with other chaperone assemblies such as Hsp90, Hsp104, and GroEL/ES (1-3). Central to Hsp70 function is its ATP-dependent interaction with client proteins, facilitated by Hsp40 cochaperones and nucleotide exchange factors (NEFs) (4). Hsp70 is a weak ATPase that recognizes and binds substrates at sites containing large aliphatic hydrophobic residues, Ile, Leu, and Val, flanked by positively charged amino acids such as Arg and Lys (5). Initial binding of substrate to the ATP-form of Hsp70 can occur directly, or via Hsp40, with rapid on/off kinetics that give rise to a weak overall affinity for the interaction. Subsequent ATP hydrolysis, stimulated by interactions with Hsp40 and substrate, leads to a large conformational change in the chaperone, locking the substrate in the Hsp70 bound state. The resulting complex is of high affinity with slow substrate on/off rates (2).Escherichia coli DnaK is the best studied of Hsp70 chaperones. It is a 70-kDa protein comprised of an N-terminal ATPase and a C-terminal substrate binding domain that communicate allosterically to couple ATP hydrolysis with substrate binding (3). Highresolution structures of ADP-(6) and ATP-DnaK (7, 8) establish that these two domains dock on to one another in the ATP-DnaK state, but become detached from each other in the ADP-bound form. In contrast to the detailed structural studies characterizing DnaK, little atomic...

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Section: Discussionmentioning

confidence: 99%

Hsp70 biases the folding pathways of client proteins

Sekhar

Rosenzweig

Bouvignies

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…CABS is a well-established modeling tool extensively tested in many applications, including the folding and binding mechanism of an intrinsically disordered peptide36, folding mechanisms of globular proteins from the denatured to the folded state373839, simulation of protein dynamics, near-native structure fluctuations4041 and protein structure prediction4243. In the CABS-dock automated protocol1011, CABS coarse-grained simulation is merged with the all-atom local optimization of selected reconstructed models.…”

Section: Methodsmentioning

confidence: 99%

Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction

Ciemny

Dębiński

Paczkowska

et al. 2016

Sci Rep

Self Cite

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Protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design. Experimental data suggest that p53-MDM2 binding is affected by significant rearrangements of a lid region - the N-terminal highly flexible MDM2 fragment; however, the details are not clear. The large size of the highly flexible MDM2 fragments makes p53-MDM2 intractable for exhaustive binding dynamics studies using atomistic models. We performed extensive dynamics simulations using the CABS-dock method, including large-scale structural rearrangements of MDM2 flexible regions. Without a priori knowledge of the p53 peptide structure or its binding site, we obtained near-native models of the p53-MDM2 complex. The simulation results match well the experimental data and provide new insights into the possible role of the lid fragment in p53 binding. The presented case study demonstrates that CABS-dock methodology opens up new opportunities for protein-peptide docking with large-scale changes of the protein receptor structure.

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“…To reduce the computational burden during molecular simulations coarse‐grained (CG) models have been developed that represent the protein or peptide by a smaller number of sites compared with a full atomistic (AT) description 2–19. A variety of CG models have been developed that differ in the number of interacting sites and the form of the force field to model effective bonded and nonbonded interactions (reviewed in Refs 16–19…”

Section: Introductionmentioning

confidence: 99%

Combining coarse‐grained nonbonded and atomistic bonded interactions for protein modeling

Zacharias

2012

Proteins

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A hybrid coarse-grained (CG) and atomistic (AT) model for protein simulations and rapid searching and refinement of peptide-protein complexes has been developed. In contrast to other hybrid models that typically represent spatially separate parts of a protein by either a CG or an AT force field model, the present approach simultaneously represents the protein by an AT (united atom) and a CG model. The interactions of the protein main chain are described based on the united atom force field allowing a realistic representation of protein secondary structures. In addition, the AT description of all other bonded interactions keeps the protein compatible with a realistic bonded geometry. Nonbonded interactions between side chains and side chains and main chain are calculated at the level of a CG model using a knowledge-based potential. Unrestrained molecular dynamics simulations on several test proteins resulted in trajectories in reasonable agreement with the corresponding experimental structures. Applications to the refinement of docked peptide-protein complexes resulted in improved complex structures. Application to the rapid refinement of docked protein-protein complex is also possible but requires further optimization of force field parameters.

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Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation–Condensation to Framework Mechanism

Cited by 39 publications

References 39 publications

Hsp70 biases the folding pathways of client proteins

Hsp70 biases the folding pathways of client proteins

Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction

Combining coarse‐grained nonbonded and atomistic bonded interactions for protein modeling

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